{"id":21476,"library":"itk-segmentation","title":"ITK Segmentation","description":"ITK is an open-source, cross-platform toolkit for N-dimensional image analysis, segmentation, and registration. The itk-segmentation subpackage provides segmentation algorithms, including level sets, watershed, region growing, and threshold-based methods. Current version 5.4.6 requires Python >=3.8, with ongoing development toward ITK 6.0 (currently in beta). Regular maintenance releases occur approximately quarterly.","status":"active","version":"5.4.6","language":"python","source_language":"en","source_url":"https://github.com/InsightSoftwareConsortium/ITK","tags":["medical imaging","image segmentation","image analysis","n-dimensional"],"install":[{"cmd":"pip install itk-segmentation","lang":"bash","label":"Install from PyPI"}],"dependencies":[],"imports":[{"note":"ITK uses a top-level Python module 'itk' and nested classes; never import subpackages directly.","wrong":"from itkSegmentation import SegmentationLevelSetImageFilter","symbol":"itk.SegmentationLevelSetImageFilter","correct":"import itk"},{"note":"ImageFileReader is a template class; you must specify the image type via brackets.","wrong":"from itk import ImageFileReader","symbol":"ImageFileReader","correct":"import itk; reader = itk.ImageFileReader[type].New()"}],"quickstart":{"code":"import itk\n\n# Read an image (replace with actual file path or use a sample image)\nimage = itk.imread('input.nii.gz', itk.F)\n\n# Apply binary threshold segmentation\nsegmented = itk.binary_threshold_image_filter(\n    image,\n    lower_threshold=100,\n    upper_threshold=500,\n    inside_value=255,\n    outside_value=0\n)\n\n# Write result\nitk.imwrite(segmented, 'segmented.nii.gz')","lang":"python","description":"Reads an image, applies a binary threshold, and writes the segmentation."},"warnings":[{"fix":"For quick scripting use itk.function_name; for advanced control use itk.ClassName.New()","message":"ITK uses snake_case for simple filter wrappers (e.g., itk.binary_threshold_image_filter) but PascalCase for full filter classes (e.g., itk.BinaryThresholdImageFilter).","severity":"gotcha","affected_versions":"5.x"},{"fix":"Ensure your build environment supports C++17. Consider using conda or pre-built wheels if available.","message":"ITK 6.0 requires C++17 compiler; not all legacy systems have it. Python wheels may not be available for all platforms.","severity":"breaking","affected_versions":">=6.0"},{"fix":"Use itk.imread/imwrite without specifying ImageIO. If needed, use itk.ImageIOFactory.CreateImageIO and set manually.","message":"ImageIO factory classes like itk.GDCMImageIO are replaced by itk.GDCMImageIO.New() or automatically detected.","severity":"deprecated","affected_versions":"5.x"},{"fix":"Explicitly specify pixel type: itk.imread('file', itk.F) reads as float.","message":"itk.imread assumes fixed integer types (e.g., itk.UC for unsigned char). For floating point, use itk.F or itk.D.","severity":"gotcha","affected_versions":"5.x"},{"fix":"Always provide the image types when using class-based filters; use simple wrappers for convenience.","message":"Template parameters in ITK are specified via brackets: filter = itk.BinaryThresholdImageFilter[InputImageType, OutputImageType].New()","severity":"gotcha","affected_versions":"5.x"}],"env_vars":null,"last_verified":"2026-04-27T00:00:00.000Z","next_check":"2026-07-26T00:00:00.000Z","problems":[{"fix":"Use functional interface: itk.segmentation_level_set_image_filter(...) or import the specific filter via itk.LevelSetExtension.LevelSetExtensionBase.","cause":"ITK's Python module does not expose all C++ classes directly; some require loading submodules or using different names.","error":"AttributeError: module 'itk' has no attribute 'SegmentationLevelSetImageFilter'"},{"fix":"Install the 'itk' metapackage or use conda: conda install -c conda-forge itk","cause":"Missing ITK shared libraries in the system's library path.","error":"RuntimeError: ImportError: libitkcommon.so.6: cannot open shared object file"},{"fix":"Check that template types and dimensions match. For example: itk.CastImageFilter[InputType, OutputType].New()","cause":"Passing an invalid argument to a filter's New method, often due to wrong template type.","error":"TypeError: in method 'New', argument 1 of type 'itk::ImageIOBase::Pointer'"},{"fix":"Use itk.GetArrayFromImage to get a numpy array, then squeeze: np.squeeze(array) if needed.","cause":"ITK expects 2D image arrays for 2D images, not 3D with singleton dimension.","error":"ValueError: could not broadcast input array from shape (512,512) into shape (512,512,1)"}],"ecosystem":"pypi","meta_description":null,"install_score":null,"install_tag":null,"quickstart_score":null,"quickstart_tag":null}